Cytochrome c oxidase barcodes for aquatic oligochaete identification: development of a Swiss reference database.

Régis Vivien,Maria Holzmann,Inge Werner,Michel Lafont,Benoit J.D Ferrari,Jan Pawlowski

doi:10.7717/peerj.4122

Abstract

IntroductionAquatic oligochaetes represent valuable indicators of the quality of sediments of watercourses and lakes, but their difficult identification based on morphological criteria compromises their more common use for eco-diagnostic analyses. This issue could be overcome by using DNA barcodes for species identification. A 10% threshold of cytochrome c oxidase (COI) divergence was proposed for differentiating between oligochaete species based on molecular and morphological data. A Swiss database of COI sequences of aquatic oligochaetes was initiated in 2012. The aim of this study is to complement the Swiss oligochaete database of COI sequences and to confirm the relevance of this threshold for species delimitation.MethodsWe sequenced the COI sequence of 216 specimens collected in different regions of Switzerland and ITS2 region of some lineages whose delimitation with COI data was doubtful.ResultsWe distinguished 53 lineages, among which 34 were new for Switzerland and 17 sequenced for the first time. All the lineages were separated by more than 10% of COI variation, with the exception of some species within Nais and Uncinais. In these two genera, the threshold was lowered to 8% to be congruent with the morphological analysis. The total number of lineages reported so far for Switzerland is 75, including 59 morphospecies or unidentified species and 16 cryptic species.DiscussionOur study shows that the threshold of 10% of COI divergence is generally appropriate to distinguish aquatic oligochaete lineages, but that it must be adjusted for some species. The database reported here will be complemented in the future in parallel to the development of genetic oligochaete indices.

Highlights

Aquatic oligochaetes represent valuable indicators of the quality of sediments of watercourses and lakes, but their difficult identification based on morphological criteria compromises their more common use for eco-diagnostic analyses
The minimal interlineage variation of the species Nais christinae and Nais stolci/pardalis was slightly >10%, while it was between 8.1 and 9 for the species Nais alpina, Nais communis, Nais pseudobtusa and Uncinais uncinata. These lineages were clearly differentiated by the morphological analysis and so the threshold of genetic variation of c oxidase (COI) to discriminate the species in these two genera was fixed at 8%
The ITS2 sequences of the specimens diverging in COI by 10.7% were identical

Summary

Introduction

Aquatic oligochaetes represent valuable indicators of the quality of sediments of watercourses and lakes, but their difficult identification based on morphological criteria compromises their more common use for eco-diagnostic analyses. This issue could be overcome by using DNA barcodes for species identification. Freshwater oligochaetes include a large number of species showing a wide range of tolerance to chemical pollution (Rodriguez & Reynoldson, 2011) For some decades they have been used in many countries for assessing the biological quality of river and lake sediments. Many aquatic oligochaetes include cryptic species undetectable morphologically (e.g., Beauchamp et al, 2001; Gustafsson, Price & Erséus, 2009; Bely & Wray, 2004)

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